Sequence
atgc intronic sequence ATGC exonic sequencegtaagaatctgcgcaaaaagttgtctatcttatacttaaatttatgattaatgtatatgatttttgtgtatattgaattccttgttaacagGCTCCTTCAACTGAAATAGCTGTTTTAGATCTTCAACATGCAACAGCTGAAGTTAGTGAAATAGTATTTTTCTTGCTTGGCGCAATGACCATTGTGGAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G19490.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G19490.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os09g02214.1 (Oryza sativa), 3'ss of exon 3
-----------gtaagaatctgcgcaaaaagttgtctatcttatacttaaatttatgattaatgtatatgatttttgtgtatattgaattccttgttaa----cagGCTCCTTCAACTGAAATAGCTGTTTTAGATCTTCAACATGCAACAGCTGAAGTTAGTGAAATAGTATTTTTCTTGCTTGGCGCAATGACCATTGTGGAGA
| | | ||| | | | | | || |||| | ||| | || | ||| |||| ||| || || ||| | ||||||| || ||||| |||| ||| ||| | ||| |||| || ||||||||||||||||| ||||||||||| || |||||||||||||| ||||
ttttatcacctattatattctatttactgaatcacttttttt----ttaa--tcatggtggatcacctttattgttgtctattttctgtttcttcctgcaatttagGCTCCATCTACTGATGTAGCAGTTCAAGAGTTGAGTCATACAACCGCCGAAGTTAGTGAAATAGTCTTTTTCTTGCTCGGTGCAATGACCATTGTTGAGA
upper sequence: AT3G19490.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G053927_T01 (Zea mays), 3'ss of exon 3
gtaagaat--ctgcgcaaaaagttgtctatcttatac-ttaaatttatgattaatgtatatgat----ttttgtgtatattgaattccttgttaa---cagGCTCCTTCAACTGAAATAGCTGTTTTAGATCTTCAACATGCAACAGCTGAAGTTAGTGAAATAGTATTTTTCTTGCTTGGCGCAATGACCATTGTGGAGA
|||||| || |||| | || | || || | | | ||||| |||| |||| | || || |||| | ||||||| || ||||| |||||||| ||| | || |||| |||||||||||||||| || |||||||||||||| |||||||| |||||||| |
-aaagaattgctattttgctttttgttgaaacgatccatttaaacactcttgattgtatctgatcatcttttattcttacctgtttttctgttgaatgtagGCTCCCTCGACTGATGTAGCTGTTCAAGAGTTGAGCCAGTCAACTTCTGAAGTTAGTGAAATTGTGTTTTTCTTGCTTGGTGCAATGACTATTGTGGAAA
upper sequence: AT3G19490.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G40920.1 (Glycine max), 3'ss of exon 3
--gtaagaatctgcgcaaaaagttgtctatcttatact----taaatttatg---attaatgtatatgatttttgtgtatattgaattccttgttaacagGCTCCTTCAACTGAAATAGCTGTTTTAGATCTTCAACATGCAACAGCTGAAGTTAGTGAAATAGTATTTTTCTTGCTTGGCGCAATGACCATTGTGGAGA
| | | ||| | | ||| | | || | | ||||| ||| | || | ||| | | | ||| || | | ||||||| |||||||| |||||||||| ||| ||| ||||||| | || ||||| ||||||||||| |||||||||||||| |||||||||||||| ||||
aaatgatggtttgcctactgatatgttagttacagacactggtcagtttatttatatttttacattttgaggttgcttgtctccctttctttatctatagGCTCCATCAACTGATATAGCTGTTTCAGAGCTTACACATGCATCTGCAGAAGTCAGTGAAATAGTGTTTTTCTTGCTTGGTGCAATGACCATTGTTGAGA
upper sequence: AT3G19490.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G26380.1 (Glycine max), 3'ss of exon 3
-gtaagaatctgcgcaa---aaagttgtctatcttatacttaaatttatgattaatgtat-----atgatttttgtgtatattgaattccttgttaacagGCTCCTTCAACTGAAATAGCTGTTTTAGATCTTCAACATGCAACAGCTGAAGTTAGTGAAATAGTATTTTTCTTGCTTGGCGCAATGACCATTGTGGAGA
| |||| || |||| || | ||| || ||||| | | | |||| | | ||| || |||| | ||||||| |||||||| |||||||||| ||| ||| ||||||| | | ||||| ||||||||||| |||||||||||||| |||||||||||||| ||||
tatttatatctttacattttgaagtcgtttgtctcccttgctttcttttgattggattttccaccactatttgctttttatttgtatggattgtctatagGCTCCATCAACTGATATAGCTGTTTCAGAGCTTACACATGCATCTGTGGAAGTCAGTGAAATAGTGTTTTTCTTGCTTGGTGCAATGACCATTGTTGAGA
upper sequence: AT3G19490.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G26550.1 (Glycine max), 3'ss of exon 1
------gtaagaatctgcgcaaaaagttgtctatcttatacttaaatttat--gattaatgtatatgatttttgtgtatattgaattc-cttgttaacagGCTCCTTCAACTGAAATAGCTGTTTTAGATCTTCAACATGCAACAGCTGAAGTTAGTGAAATAGTATTTTTCTTGCTTGGCGCAATGACCATTGTGGAGA
||||| | || | ||||| | ||| || || |||| | ||| | ||| | || |||| | ||||||| |||||||| |||||||||| ||| || |||||| | || ||||| ||||||||||| |||||||||||||| |||||||||||||| ||||
ctgattgtaagtctacattttgaagtcattttatctccttctttctttgattggattttccattgctgtttgcttttattctttatggatttgtctatagGCTCCATCAACTGATATAGCTGTTTCAGAGCTAACTCATGCATCTGCAGAAGTCAGTGAAATAGTGTTTTTCTTGCTTGGTGCAATGACCATTGTTGAGA
upper sequence: AT3G19490.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv03s0180g00120.t01 (Vitis vinifera), 3'ss of exon 3
-------gtaagaatctgcgcaaaaagttgtctatcttatactt---aaatttatgattaatgtatatgatttttgtgtatattgaattccttgttaacagGCTCCTTCAACTGAAATAGCTGTTTTAGATCTTCAACATGCAACAGCTGAAGTTAGTGAAATAGTATTTTTCTTGCTTGGCGCAATGACCATTGTGGAGA
| | || | | || || || ||| | || | ||| | ||| | | |||| | || || | || || ||||| |||| ||||||||||| |||||||||| ||| || |||||| | |||||||||||||||||||| |||||||||||||| |||||||||||||| ||||
ccattggatcaatatatccattgaattttcattaatttaaattttgcacattgagtcttactttttatg-tgttaatgcttgtttctgtctttgtttgtagGCACCTTCAACTGATATAGCTGTTTCAGAGCTAACTCATGCATCTGCTGAAGTTAGTGAAATAGTGTTTTTCTTGCTTGGTGCAATGACCATTGTTGAGAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|124976456|gb|EL049872.1|EL049872EST: GAATAGGACTTTTGATGGCTGTGAGTTTGTGGGTTGTGCGGAGCATAGGG GCTCCTTCAACTGAAATAACTGTTTTAGATCTT
genomic: GAATAGGACTTTTGATGGCTGTGAGTTTGTGGGTTGTGCGGAGCATAGGGgtaagaatct ... ttgttaacagGCTCCTTCAACTGAAATAGCTGTTTTAGATCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaatttatgattaatgtatatgatttttgtgtatattgaattccttgttaacagGCTCCTTCAACTGAAATAGCTGTTTTAGATCTTCAACATGCAACAGCTGAAGTTAGTGAAATAGTATTTTTCTTGCTTGGCGCAATGACCATTGTGGAGA
gattaat putative branch site (score: 3)
ttccttgtt putative PPT
attaatgtatatgatt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaatctgcgcaaaaagttgtctatcttatacttaaatttatgattaatgtatatgatttttgtgtatattgaattccttgttaacagGCTCCTTCAACTGAAATAGCTGTTTTAGATCTTCAACATGCAACAGCTGAAGTTAGTGAAATAGTATTTTTCTTGCTTGGCGCAATGACCATTGTGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA